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The nucleosome repeat length (NRL) is an integral chromatin property important for its biological functions. Recent experiments revealed several conflicting trends of the NRL dependence on the concentrations of histones and other architectural chromatin proteins, both in vitro and in vivo, but a systematic theoretical description of NRL as a function of DNA sequence and epigenetic determinants is currently lacking. To address this problem, we have performed an integrative biophysical and bioinformatics analysis in species ranging from yeast to frog to mouse where NRL was studied as a function of various parameters. We show that in simple eukaryotes such as yeast, a lower limit for the NRL value exists, determined by internucleosome interactions and remodeler action. For higher eukaryotes, also the upper limit exists since NRL is an increasing but saturating function of the linker histone concentration. Counterintuitively, smaller H1 variants or non-histone architectural proteins can initiate larger effects on the NRL due to entropic reasons. Furthermore, we demonstrate that different regimes of the NRL dependence on histone concentrations exist depending on whether DNA sequence-specific effects dominate over boundary effects or vice versa. We consider several classes of genomic regions with apparently different regimes of the NRL variation. As one extreme, our analysis reveals that the period of oscillations of the nucleosome density around bound RNA polymerase coincides with the period of oscillations of positioning sites of the corresponding DNA sequence. At another extreme, we show that although mouse major satellite repeats intrinsically encode well-defined nucleosome preferences, they have no unique nucleosome arrangement and can undergo a switch between two distinct types of nucleosome positioning.
We show that moderate energy relaxation in the formation of dark matter halos invariably leads to profiles that match those observed in the central regions of galaxies. The density profile of the central region is universal and insensitive to either the seed perturbation shape or the details of the relaxation process. The profile has a central core; the multiplication of the central density by the core radius is almost independent of the halo mass, in accordance with observations. In the core area the density distribution behaves as an Einasto profile with low index (n similar to 0.5); it has an extensive region with rho proportional to r(-2) at larger distances. This is exactly the shape that observations suggest for the central region of galaxies. On the other hand, this shape does not fit the galaxy cluster profiles. A possible explanation of this fact is that the relaxation is violent in the case of galaxy clusters; however, it is not violent enough when galaxies or smaller dark matter structures are considered. We discuss the reasons for this.
We argue that the theories of Volokitin and Persson (2014 New J. Phys. 16 118001), Dedkov and Kyasov (2008 J. Phys.: Condens. Matter 20 354006), and Pieplow and Henkel (2013 New J. Phys. 15 023027) agree on the electromagnetic force on a small, polarizable particle that is moving parallel to a planar, macroscopic body, as far as the contribution of evanescent waves is concerned. The apparent differences are discussed in detail and explained by choices of units and integral transformations. We point out in particular the role of the Lorentz contraction in the procedure used by Volokitin and Persson, where a macroscopic body is 'diluted' to obtain the force on a small particle. Differences that appear in the contribution of propagating photons are briefly mentioned.
Anomalous diffusion is frequently described by scaled Brownian motion (SBM){,} a Gaussian process with a power-law time dependent diffusion coefficient. Its mean squared displacement is ?x2(t)? [similar{,} equals] 2K(t)t with K(t) [similar{,} equals] t[small alpha]-1 for 0 < [small alpha] < 2. SBM may provide a seemingly adequate description in the case of unbounded diffusion{,} for which its probability density function coincides with that of fractional Brownian motion. Here we show that free SBM is weakly non-ergodic but does not exhibit a significant amplitude scatter of the time averaged mean squared displacement. More severely{,} we demonstrate that under confinement{,} the dynamics encoded by SBM is fundamentally different from both fractional Brownian motion and continuous time random walks. SBM is highly non-stationary and cannot provide a physical description for particles in a thermalised stationary system. Our findings have direct impact on the modelling of single particle tracking experiments{,} in particular{,} under confinement inside cellular compartments or when optical tweezers tracking methods are used.
Anomalous diffusion is frequently described by scaled Brownian motion (SBM){,} a Gaussian process with a power-law time dependent diffusion coefficient. Its mean squared displacement is ?x2(t)? [similar{,} equals] 2K(t)t with K(t) [similar{,} equals] t[small alpha]-1 for 0 < [small alpha] < 2. SBM may provide a seemingly adequate description in the case of unbounded diffusion{,} for which its probability density function coincides with that of fractional Brownian motion. Here we show that free SBM is weakly non-ergodic but does not exhibit a significant amplitude scatter of the time averaged mean squared displacement. More severely{,} we demonstrate that under confinement{,} the dynamics encoded by SBM is fundamentally different from both fractional Brownian motion and continuous time random walks. SBM is highly non-stationary and cannot provide a physical description for particles in a thermalised stationary system. Our findings have direct impact on the modelling of single particle tracking experiments{,} in particular{,} under confinement inside cellular compartments or when optical tweezers tracking methods are used.
Although it is now understood that chaos in complex classical systems is the foundation of thermodynamic behavior, the detailed relations between the microscopic properties of the chaotic dynamics and the macroscopic thermodynamic observations still remain mostly in the dark. In this work, we numerically analyze the probability of chaos in strongly nonlinear Hamiltonian systems and find different scaling properties depending on the nonlinear structure of the model. We argue that these different scaling laws of chaos have definite consequences for the macroscopic diffusive behavior, as chaos is the microscopic mechanism of diffusion. This is compared with previous results on chaotic diffusion [M. Mulansky and A. Pikovsky, New J. Phys. 15, 053015 (2013)], and a relation between microscopic chaos and macroscopic diffusion is established. (C) 2014 AIP Publishing LLC.
We report a process for preparing polymer ferroelectrets by means of screen printing-a technology that is widely used for the two-dimensional patterning of printed layers. In order to produce polymer-film systems with cavities that are suitable for bipolar electric charging, a screen-printing paste is deposited through a screen with a pre-designed pattern onto the surface of a polymer electret film. Another such polymer film is placed on top of the printed pattern, and well-defined cavities are formed in-between. During heating and curing, the polymer films are tightly bonded to the patterned paste layer so that a stable three-layer system is obtained. In the present work, polycarbonate (PC) films have been employed as electret layers. Screen printing, curing and charging led to PC ferroelectret systems with a piezoelectric d (33) coefficient of about 28 pC/N that is stable up to 100 C-a similar to. Due to the rather soft patterned layer, d (33) strongly decreases already for static pressures of tens of kPa. The results demonstrate the suitability of screen printing for the preparation of ferroelectret systems.
Search for dark matter annihilation signatures in HESS observations of
dwarf spheroidal galaxies
(2014)
Dwarf spheroidal galaxies of the Local Group are close satellites of the Milky Way characterized by a large mass-to-light ratio and are not expected to be the site of nonthermal high-energy gamma-ray emission or intense star formation. Therefore they are among the most promising candidates for indirect dark matter searches. During the last years the High Energy Stereoscopic System (H.E.S.S.) of imaging atmospheric Cherenkov telescopes observed five of these dwarf galaxies for more than 140 hours in total, searching for TeV gamma-ray emission from annihilation of dark matter particles. The new results of the deep exposure of the Sagittarius dwarf spheroidal galaxy, the first observations of the Coma Berenices and Fornax dwarves and the reanalysis of two more dwarf spheroidal galaxies already published by the H.E.S.S. Collaboration, Carina and Sculptor, are presented. In the absence of a significant signal new constraints on the annihilation cross section applicable to weakly interacting massive particles (WIMPs) are derived by combining the observations of the five dwarf galaxies. The combined exclusion limit depends on the WIMP mass and the best constraint is reached at 1-2 TeV masses with a cross-section upper bound of similar to 3.9 x 10(-24) cm(3) s(-1) at a 95% confidence level.
Context. Very-high-energy (VHE; E > 100 GeV) gamma-ray emission from blazars inevitably gives rise to electron-positron pair production through the interaction of these gamma-rays with the extragalactic background light (EBL). Depending on the magnetic fields in the proximity of the source, the cascade initiated from pair production can result in either an isotropic halo around an initially- beamed source or a magnetically- broadened cascade :aux.
Aims. Both extended pair-halo (PH) and magnetically broadened cascade (MBC) emission from regions surrounding the blazars 1ES 1101-232, IRS 0229+200, and PKS 2155-304 were searched for using VHE y-ray data taken with the High Energy Stereoscopic System (HESS.) and high-energy (HE; 100 MeV < E < 100 GeV) gamma-ray data with the Fermi Large Area Telescope (LAT).
Methods. By comparing the angular distributions of the reconstructed gamma-ray events to the angular profiles calculated from detailed theoretical models, the presence of PH and MBC was investigated.
Results. Upper limits on the extended emission around lES 1101-232, lES 0229+200, and PKS 2155-304 are found to be at a level of a few per cent of the Crab nebula flux above 1 TeV, depending on the assumed photon index of the cascade emission. Assuming strong extra-Galactic magnetic field (EGME) values, >10(-12) G, this limits the production of pair haloes developing from electromagnetic cascades. For weaker magnetic fields, in which electromagnetic cascades would result in MBCs. EGMF strengths in the range (0.3-3) x 10(-15) G were excluded for PKS 2155-304 at the 99% confidence level, under the assumption of a 1 Mpc coherence length.